Methanotrophic bacteria are defined by their ability to use methane as their sole source of carbon and energy. Although methanol is an obligate intermediate in the oxidation of methane, the ability to grow on methanol alone is highly variable among the obligate methanotrophs due to its toxicity (Green, Peter. Taxonomy of Methylotrophic Bacteria. In: Methane and Methanol Utilizers (Biotechnology Handbooks 5) J. Colin Murrell and Howard Dalton eds. 1992 Pleanum Press NY, pp. 23-84). Methane monooxygenase is the enzyme required for the primary step in methane activation and the product of this reaction is methanol (Murrell et al., Arch. Microbiol. (2000), 173(5-6), 325-332). This reaction occurs at ambient temperatures and pressures, whereas chemical transformation of methane to methanol requires temperatures of hundreds of degrees and high pressure (Grigoryan, E. A., Kinet. Catal. (1999), 40(3), 350-363; WO 2000007718; U.S. Pat. No. 5,750,821). It is this ability to transform methane under ambient conditions along with the abundance of methane that makes the biotransformation of methane a potentially unique and valuable process.
The commercial applications of biotransformation of methane have historically fallen broadly into three categories: 1) Production of single cell protein, (Sharpe D. H. BioProtein Manufacture (1989). Ellis Horwood series in applied science and industrial technology. New York: Halstead Press) (Villadsen, John, Recent Trends Chem. React. Eng., [Proc. Int. Chem. React. Eng. Conf.], 2nd (1987), Volume 2, 320-33. Editor(s): Kulkarni, B. D.; Mashelkar, R. A.; Sharma, M. M. Publisher: Wiley East., New Delhi, India; Naguib, M., Proc. OAPEC Symp. Petroprotein, [Pap.] (1980), Meeting Date 1979, 253-77 Publisher: Organ. Arab Pet. Exporting Countries, Kuwait, Kuwait); 2) epoxidation of alkenes for production of chemicals (U.S. Pat. No. 4,348,476); and 3) biodegradation of chlorinated pollutants (Tsien et al., Gas, Oil, Coal, Environ. Biotechnol. 2, [Pap. Int. IGT Symp. Gas, Oil, Coal, Environ. Biotechnol.], 2nd (1990), 83-104. Editor(s): Akin, Cavit; Smith, Jared. Publisher: Inst. Gas Technol., Chicago, Ill.; WO 9,633,821; Merkley et al., Biorem. Recalcitrant Org., [Pap. Int. In Situ On-Site Bioreclam. Symp.], 3rd (1995), 165-74. Editor(s): Hinchee, Robert E; Anderson, Daniel B.; Hoeppel, Ronald E. Publisher: Battelle Press, Columbus, Ohio.: Meyer et al., Microb. Releases (1993), 2(1), 11-22). Only epoxidation of alkenes has experienced little commercial success due to low product yields, toxicity of products and the large amount of cell mass required to generate products.
Large-scale protein production from methane, termed single cell protein or SCP has been technically feasible and commercialized at large scale (Villadsen supra). However, SCP has been less than economically successful due to the relatively high cost to produce microbial protein compared to agriculturally derived protein (i.e. soy protein). Single cell protein is a relatively low value product and therefore economic production cannot tolerate heavy bioprocessing costs. For this reason the yield of the methanotrophic strain may be critical to the overall economic viability of the process. Microbial biomass produced by methanotrophic bacteria is typically very high in protein content (˜70-80% by weight), which can restrict the direct use of this protein to certain types of animal feed.
The conversion of C1 compounds to complex molecules with C—C bonds is a difficult and capital intensive process by traditional chemical synthetic routes. Traditionally, methane is first converted to synthesis gas (mixtures of hydrogen, carbon monoxide and carbon dioxide), which is then used to produce other small molecular weight industrial precursors. Typically these are “commodity” type chemicals such as acetate, formaldehyde, or methanol. The basic problem is activation of the methane molecule which is thermodynamically very difficult to achieve by chemical means. “Activation” refers to the process of making the chemically unreactive methane molecule more reactive.
Methanotrophic bacteria contain enzymes (methane monooxygenases) which are capable of methane activation at ambient temperatures and pressures. Methane activation consists of oxygen insertion into methane to form methanol which is much more readily metabolized to more complex molecules within the cell. Two types of methane monooxygenase are found in methanotrophic bacteria. A particulate methane monooxygenase (pMMO) has a narrow substrate specificity and is incapable of oxygen insertion into more complex molecules. Some, but not all methanotrophs may also contain a soluble methane monooxygenase (sMMO). This enzyme has been the subject of much investigation and proprietary claims due to its ability to oxygenate, or functionalize, a wide variety of aliphatic and aromatic molecules. This characteristic has been utilized for co-metabolic production processes where methanotrophs are fed both methane and a more complex molecule to be transformed by the sMMO. Numerous examples are reported of processes requiring both methane and, typically, a petroleum-derived feedstock such as toluene, naphthalene, or decane, where sMMO plays a role. However, the art is silent with respect to using methanotrophs for net synthesis of chemicals from methane as opposed to these co-metabolic transformations. For net synthesis, only inexpensive methane is required along with the ability to genetically engineer the strain to produce the desired chemical.
Methanotrophic cells can further build the oxidation products of methane (i.e. methanol and formaldehyde) into more complex molecules such as protein, carbohydrate and lipids. For example, under certain conditions methanotrophs are known to produce exopolysaccharides (Ivanova et al., Mikrobiologiya (1988), 57(4), 600-5; Kilbane, John J., II Gas, Oil, Coal, Environ. Biotechnol. 3, [Pap. IGT's Int. Symp.], 3rd (1991), Meeting Date 1990, 207-26. Editor(s): Akin, Cavit; Smith, Jared. Publisher: IGT, Chicago, Ill.). Similarly, methanotrophs are known to accumulate both isoprenoid compounds and carotenoid pigments of various carbon lengths (Urakami et al., J. Gen. Appl. Microbiol. (1986), 32(4), 317-41). Although these compounds have been identified in methanotrophs, they have not been microbial platforms of choice for production as these organisms have very poorly developed genetic systems, thereby limiting metabolic engineering for chemicals.
A necessary prerequisite to metabolic engineering of methanotrophs is a full understanding, and optimization, of the carbon metabolism for maximum growth and/or product yield. Obligate methanotrophs are typically thought to channel carbon from methane to useful products and energy via the Entner-Douderoff Pathway which utilizes the keto-deoxy phosphogluconate aldolase enzyme (Dijkhuizen, L., P. R. Levering, G. E. DeVries 1992. In: Methane and Methanol Utilizers (Biotechnology Handbooks 5) J. Colin Murrell and Howard Dalton eds. 1992 Pleanum Press NY pp 149-181). This pathway is not energy-yielding as is the case for the Embden-Meyerhof pathway. Thus, utilization of the Entner-Douderoff pathway results in lower cellular production yields and a greater proportion of the carbon produced as carbon dioxide compared to organisms that use the Embden-Meyerhof pathway. Therefore, a more energy efficient carbon processing pathway would greatly enhance the commercial viability of a methanotrophic platform for the generation of materials.
As noted above, methanotrophic bacteria possess the potential to be commercially effective production platforms for materials such as single cell protein, exopolysaccharides, and long chain carbon molecules such as isoprenoids and carotenoid pigments. The usefulness of methanotrophs for production of a larger range of chemicals is constrained however, by several limitations including, relatively slow growth rates of methanotrophs, limited ability to tolerate methanol as an alternative substrate to methane, difficulty in genetic engineering, poor understanding of the roles of multiple carbon assimilation pathways present in methanotrophs, and potentially high costs due to the oxygen demand of fully saturated substrates such as methane. The problem to be solved therefore is to develop a fast-growing, high yielding methanotroph capable of receiving foreign genes via standard genetic procedures. Full and rapid resolution of central carbon pathways is essential for enabling pathway engineering and carbon flux management for new products.
Applicants have solved the stated problem by providing a methanotrophic bacterial strain capable of efficiently using either methanol or methane as a carbon substrate. The strain is also metabolically versatile in that it contains multiple pathways for the incorporation of carbon from formaldehyde into 3-C units. The discovery of a phosphofructokinase and fructose 1,6bisphosphate aldolase in this strain suggests that it can utilize the more energetically favorable Embden-Meyerhof pathway in addition to the Entner-Douderoff pathways. The present strain is shown to be useful for the production of a variety of materials beyond single cell protein to include carbohydrates, pigments, terpenoid compounds and aromatic compounds. The formation of large amounts of carbohydrates from methane or methanol can be carried out by this strain. This is surprising and also enables this strain to be used for the production of typical carbohydrate or sugar fermentation end-products such as alcohols, acids and ketones. The present strain was also shown to be capable of genetic exchange with donor species such as Escherichia coli via a standard genetic procedure known as bacterial conjugation. In this way, the strain can be engineered for net synthesis from methane to produce new classes of products other than those naturally produced.